Hi, there are a few different shopping cart options that will use Amazon’s MWS API to send orders for FBA. They also support Amazon Payments (Checkout by Amazon).
I have used 3D Cart, which supports it.
I am aware that BigCommerce Magento supports it as well.
This has nothing to do with the Affiliate network, but uses your Amazon MWS credentials.
The Affiliate network is a widget you can put on your website for Amazon ads which you get paid for. I have looked into it, but don’t think diverting customers I paid for to Amazon to buy something I don’t sell is worth my advertising spend (PPC, SEO).
You don’t require the Affiliate network to sell your own items. You just create them on your website (titles, descriptions, images). You will probably need to re-enter the content (copy/paste) unless you subscribe to a service that can provide that for you.
When a customer purchases on your FBA enabled website, you will pay Amazon Multichannel Fulfillment Fees ($4.75 per order, $0.75 per item, $0.45 per pound). Additions for oversized, expedited or priority shipping may apply).
You can advertise on Amazon using Product Ads, Google Shopping, other comparison shopping sites, or Google and Bing search. These all have per item click fees.
There is no conflict of interest because Amazon is not helping you with customer acquisition. You need to do that yourself.